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On Birth Island, Giovanni hollers that he shall gain possession of Deoxys's space powers, and orders Aggron to charge forward. However, before the giant steel Pokémon manages to make contact, Deoxys orbs away together with its pyramid-like barrier and reappears at another spot. Giovanni grins that the creature is using teleport, and muses that its special black delta shield not only restores its strength from within, but also acts as a protective wall to external attacks. Yet, he has already figured out the ways to counter all these defensive skills of Deoxys, and sends out Beedrill from its Pokéball.

The poison bee quickly brings its speed to the maximum by using agility, and begins fervently chasing after Deoxys's teleporting delta shield. With each pursuit, Beedrill makes sure that it is taking the shortest path, and soon causes the pyramid-like structure to heat up in red. Deoxys gradually gets cornered back to the center of the island, where Aggron has been waiting all this time to strike, and the iron armour Pokémon immediately grasps the chance to thrust its horns forward for a brickbreak.

The attack instantly shatters the black shield, and Giovanni swiftly tosses out a Pokéball which has the word DNA carved on it. A powerful attraction field from the ball spans out to render Deoxys incapable of struggling, and the creature lets out a shriek as it hopelessly gets caught.

Walking over to pick up his newest capture, Giovanni grins evilly at his victory, and remarks that with the help of this specially designed Pokéball, he is finally able to gain possession of the space-born Pokémon's powers. It turns out that the delta shield of Deoxys is actually created by a combination of the moves reflect and lightscreen, and brickbreak, which specifically deals with such defensive barriers, is the ideal attack to crack it.

The TR leader smirks that it is all attributed to the intensive investigations and observations they did to study Deoxys's fighting patterns, the characteristics of its different forms, its skills as well as many other important factors. Taking out a dark coloured Pokedex which is identical to the one Jagura holds, he thinks to himself that perhaps he should thank Red the most, as he wouldn't have succeeded in capturing Deoxys without the boy's input.

Earlier, when Storc unleashed the powers of the Ruby and Sapphire stone plates on Five Island, the gems' special energies have radiated out to cover the entire Sevii Islands, mimicking the unique climate of Hoenn and enabling Deoxys to fully activate its four forms, normal, attack, defence and speed. Now that the DNA Pokémon is capable of freely morphing between its various states, it can be officially declared as complete.

Back at the Team Rocket Warehouse on Five Island, Storc has witnessed Giovanni's capturing of Individual 2 from the real time images transferred back by the ! and ? Unown eye-cameras, and marvels at their boss's greatness. She turns to Jagura and states that it is time to proceed to the next stage of their plan, but the little man didn't manage to hear her as he is too consumed with the photo he discovered. Storc impatiently barks at him, and Jagura instantly bolts up. Storc tells him not to daydream all the time, and Jagura hurriedly trails after the tall woman while stuffing the picture into his back pocket.

Meanwhile, under the dim morning light, Red is still wandering aimlessly around Five Island with Pika in his arms. Near the rocky shore where they built their fire the night before, he sees Green and the Sea Gallop sailor studying a map of the entire Sevii Islands, and overhears them discussing about the possible places where Prof. Oak is held captive. He walks by the severely damaged PokemonCenter, and notices that Bill is also busy repairing the Pokemon Storage and Transfer System. He then hears a ruffling sound in the woods next to him, and finds Blue and Turtley training hard under Brinca to learn the water type ultimate attack, hydrocannon.

Turning his back away from all of this, Red realizes that Green and Blue are both fighting for the sake of their families, Green for his kidnapped grandfather, Prof. Oak, and Blue for her parents whose location is still unknown following their disappearance into the black hole on the Sea Gallop. Yet, the boy wonders to himself, what exactly is his reason to fight?
Ever since this new enemy, Deoxys, started its ambush on them, he has been determined to face it despite not knowing anything about the Pokémon. All along, this blind determination is the only thing that has kept him going. However, following his defeat to Deoxys, this burning motivation seems to have died out, and he wonders if it is why he is now running away from the battle.

The instant Pika hears this statement, it hops off from Red's arms, and stares back at him with a frown. Red realizes that he is simply giving excuses for himself, and Pika knows it well that it is not the real reason. He sighs that he cannot fool Pika as they have been together for so long, and after a moment of thought, decides that he shall confess to the electric rat what he really feels, something he has not revealed to either Green or Blue, that deep inside, he is actually frightened.

Back when Deoxys was about to appear on Five Island, Red felt a powerful sensation suddenly surging through his body, a burning tightness within that seems to cause all his blood to backflow and his heart to jump out from his mouth, a feeling which he has never experienced all his life. Just like the sense of alarm a fighter feels towards a powerful opponent, the boy knew right there and then that the enemy was approaching, While he was able to ignore this unnverving commotion during the intense battle, it resurfaced to haunt him again after the creature left.

What exactly gave rise to this sensation Red has no idea. He has no clue either what it entails or even what it is really about, but one thing he knows for sure is that it is the cause of his current fear. Just as the boy says that, Pika wiggles its little hands with a grin, and Red realizes that he has just found the answer to his question, his very own reason to fight the battle. He will fight because he is faced with a powerful enemy, he will fight because he needs to save Prof. Oak and Blue's parents, but most importantly, he will fight because he wants to find out the source of the uneasy feeling inside him, a reason for no one else but himself.

Thanking Pika for being his listener and enlightenment, Red vows that he will not turn away from the battle again, and apologizes for the cowardness he has shown. Pika joyfully hops back onto its trainer's shoulder, and the boy states that it is time to resume on the journey to search for his true self. He decides that the first thing they should do right now is to head to Seven Island to check on Loreli, and begins running back to where the others are.

Just then, a hollow voice comes on to say that Lorelei of the Elite 4 has already been saved, and Red immediately looks around to find its source. Without warning, a giant spoon appears out of nowhere, and carries a fainted Lorelei right towards him. Red gasps in shock when the silhouette of the spoon's holder materializes out from the horizon under the dim morning light, and the humannoid creature states that it fully understands what the boy is feeling as it is also on a journey to discover who it really is.

Recognizing the spoon as a weapon generated by psychic, Red gaps his mouth wide in disbelief that it is no other than the Team Rocket created genetic Pokémon which has disappeared since the battle a few years ago, Mewtwo…